[Bioperl-l] Parsing FASTA m10 output

Ioannis Kirmitzoglou IoannisKirmitzoglou at gmail.com
Tue Apr 17 09:05:37 EDT 2007


I apologize if this question has already been answered but my search came up
with no relevant results.
I am new to the FASTA program and after reading the fasta3x.doc I decided to
run it using the m10 output. The reason for doing such a choice was 

Quote from fasta3x.doc:  
     -m 10 is a new, parseable format for use with other
     programs.... 


I ran FASTA in batch mode and waited about 3-4 days for the results.
My problem is that today, when i started writing a perl script to parse the
output I realized that SearchIO doesn't supports m10 format.
Seems like I had to be more careful...
Before starting coding a module that will be able to parse the output (or
re-running FASTA with -m9 -d0 switches which will take 4 more days) I would
be really thankful if any of you knows of any other way to parse those
files?
Thanks in advance...

Ioannis Kirmitzoglou, MSc
PhD. Student,
Bioinformatics Research Laboratory
Department of Biological Sciences
University of Cyprus

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